Corrections

kumakain ba siya ng mansanas is the correct one.

It depends on the sentence order that you are using. This order is more natural and is usually used in spoken Tagalog. It is as if kumakain is the subject, although I think grammatically it is not. But it is like implying that you put more emphasis on the verb kumakain instead of the doer of the verb.
Natutulog ba siya? Is he/she sleeping?
Nagsasalita ba siya? Is he/she talking?But if you use this order:
Siya ba ay kumakain, you put ba after the subject, which is Siya. You do this because the emphasis is on Siya and you are merely describing or stating what Siya is doing. This is a more formal way of speaking.